fixed github actions for sphinx build

Author: Eli

.github/workflows/build_sphinx.yml

@@ -1,61 +1,55 @@
 name: "Sphinx: Render docs"
 
 on: 
-  # Runs on pushes targeting the default branch
   push:
     branches: ["main", "master"]
-
-  # Allows you to run this workflow manually from the Actions tab
   workflow_dispatch:
 
-# Sets permissions of the GITHUB_TOKEN to allow deployment to GitHub Pages
 permissions:
   contents: write
   pages: write
   id-token: write
 
-
-# Allow only one concurrent deployment, skipping runs queued between the run in-progress and latest queued.
-# However, do NOT cancel in-progress runs as we want to allow these production deployments to complete.
 concurrency:
   group: "pages"
   cancel-in-progress: false
 
 jobs:
-  # This workflow contains a single job called "build"
   build:
-
-    # The type of runner that the job will run on
     runs-on: ubuntu-latest
-
-    # Steps represent a sequence of tasks that will be executed as part of the job
     steps:
-      # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
       - uses: actions/checkout@v2
-
-      - name: Set up Python 3.10
+        with:
+          fetch-depth: 0
+      - name: Set up Python 3.9
         uses: actions/setup-python@v2
         with:
-          python-version: "3.10"
-
-      - name: Install dependencies
+          python-version: 3.9
+      - name: Add conda to system path
+        run: |
+          echo $CONDA/bin >> $GITHUB_PATH
+      - name: Conda build env for docs
         run: |
-          python -m pip install --upgrade pip
+          conda env create -f schimpy_env.yml
+          source $CONDA/etc/profile.d/conda.sh
+          conda activate schimpy
           pip install -r docsrc/requirements.txt
-
       - name: Build HTML
         run: |
+          source $CONDA/etc/profile.d/conda.sh
+          conda activate schimpy
           cd docsrc/
+          sphinx-apidoc --force -o . ../schimpy
+          make clean
           make html
-        
       - name: Run ghp-import
         shell: bash
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         run: |
+          source $CONDA/etc/profile.d/conda.sh
+          conda activate schimpy
           git config http.postBuffer 157286400
           git pull
-
           tree -L 2 -a
-
           ghp-import -n -p -f ./docs/html

schimpy_env.yml

@@ -1,7 +1,7 @@
 # This environment is a functional analysis environment for schimpy.
 # However the standard monolity for Bay-Delta SCHISM is schism_env.yml in the BayDeltaSCHISM package 
 # https://github.com/CADWRDeltaModeling/BayDeltaSCHISM
-name: schimpy              
+name: schimpy         
 channels:
   - conda-forge            # Note: the order listed in yaml is not enforced by conda
   - defaults               # For predictable behavior, set your conda config
@@ -36,4 +36,3 @@ dependencies:
 #    - "--editable=git+https://github.com/CADWRDeltaModeling/vtools3#egg=vtools3"
 #    - "--editable=git+https://github.com/CADWRDeltaModeling/schimpy#egg=schimpy"
 #    - "--editable=git+https://github.com/CADWRDeltaModeling/dms_datastore#egg=dms_datastore"
-

setup.py

@@ -16,7 +16,7 @@
     "geopandas",
     'vtools3>=3.8',         # moved unit_conversions to vtools, so dependent on the version where we did that
     "gdal",
-    "libgdal",  # libgdal is for calling gdal_translate in clip_dems
+    #"libgdal",  # libgdal is for calling gdal_translate in clip_dems
     "xarray",
     "netcdf4",
     "scipy",